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ORIGINAL RESEARCH published: 18 December 2018 doi: 10.3389/fmicb.2018.03122

Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China Xue Zhou 1* , Bolun Li 2 , Zhiying Guo 3 , Zhiyuan Wang 4 , Jian Luo 5 and Chunhui Lu 1* 1

State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China, 2 School of Geographic Sciences, Nanjing University of Information Science and Technology, Nanjing, China, 3 State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China, 4 Center for Eco-Environmental Research, Nanjing Hydraulic Research Institute, Nanjing, China, 5 School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States

Edited by: Andreas Ulrich, Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF), Germany Reviewed by: Marcus A. Horn, Leibniz University Hannover, Germany Huaiying Yao, Institute of Urban Environment (CAS), China *Correspondence: Xue Zhou [email protected] Chunhui Lu [email protected] Specialty section: This article was submitted to Terrestrial Microbiology, a section of the journal Frontiers in Microbiology Received: 13 August 2018 Accepted: 03 December 2018 Published: 18 December 2018 Citation: Zhou X, Li B, Guo Z, Wang Z, Luo J and Lu C (2018) Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China. Front. Microbiol. 9:3122. doi: 10.3389/fmicb.2018.03122

Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers’ distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers’ communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers’ community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers’ community compositions. Keywords: agricultural soil, mudflat, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, agricultural practice, MNTD

INTRODUCTION Estuaries are mixing zones of coastal seawater and freshwater from continental runoff, acting as a conduit for the transport, transformation and production of organic carbon and nutrients. Nitrogen pollutants, emitted from both industrial and agricultural activities such as wastewater treatment plants, chemical and manufacturing industries, and livestock farming (Chung et al., 1996;

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Niche Separation of Mudflat’s Nitrifiers

Busca and Pistarino, 2003; Kim et al., 2007), are transferred from terrestrial ecosystems to aquatic ecosystems through mudflats by gravitational movement (Likens and Bormann, 1974). Coupled nitrification-denitrification can remove a substantial percentage (10∼80%) of anthropogenic nitrogen pollution in estuary ecosystems (Seitzinger, 2008), where nitrification converts ammonia to nitrite and nitrate, which are subsequently released to the atmosphere as N2 gas via denitrification or anammox. The removal of nitrogen pollutants in estuaries is a microbially mediated process. Because different nitrogen-cycling microbes own different activities, the niche separation of nitrogen-cycling microbes in estuaries are thus of great concern (Bernhard et al., 2007, 2010; Mosier and Francis, 2008; Moin et al., 2009; Jin et al., 2011; Damashek et al., 2015; Damashek and Francis, 2017; Zhang et al., 2018). In addition, increasing human disturbance in mudflats has a significant impact on changing soil properties, such as soil carbon and nitrogen contents (Wang et al., 2010), which are key environmental factors controlling the community composition of microorganisms involved the in nitrogen cycle. The ammonia oxidation process is the first and rate-limiting step of nitrification. It is necessary to assess the potential nitrification rates and niche differentiation of ammonia oxidizers in both multiflats and adjacent agricultural soils. The study site of the current study was the Yangtze River, the third-largest river in the world, which has a high biogeochemical flux of nitrogen, discharging into the East China Sea with a nitrate load of 6.3 × 106 t/a. Intensive agricultural practice occurs in the upper estuary in Jiangsu Province, as shown in Figure 1. Ammonia oxidation is considered to be carried out in soils by ammonia oxidizing bacteria (AOB) (Kowalchuk and Stephen, 2001) and ammonia oxidizing archaea (AOA) (Leininger et al., 2006). Previous studies in open ocean environments indicated that AOA far outnumber AOB (Wuchter et al., 2006; Mincer et al., 2007; Beman et al., 2008), suggesting a high tolerance of AOA to salinity pressures (Santoro et al., 2008; Bernhard et al., 2010). However, Zhang et al. (2018) showed the equal numbers of AOA and AOB amoA genes at the soil/sediment interface, while AOB was more abundant than AOA in high salinity environments (Santoro et al., 2008). In addition, debatable results were also established in agricultural ecosystems. Many studies indicated the influence of ammonia concentration and fertilization on the niche separation of AOA and AOB, that AOB rather than AOA grew in soils treated with high levels of inorganic ammonium (Di et al., 2009, 2010; Jia and Conrad, 2009). In contrast, evidence from stable isotope probing (SIP) in paddy soils demonstrated that active AOA numerically outcompeted AOB (Wang et al., 2014). Thus, questions remain concerning their relative importance in mudflat and agricultural soils. The objectives of this study were to elucidate the differentiation of the potential nitrification rates and niche separation of community composition of ammonia oxidizers (AOA and AOB) between mudflat and adjacent agricultural soils and to investigate the potential links between the environmental variables and ammonia oxidizers’ community structure.


MATERIALS AND METHODS Sampling Two geographic sampling regions were selected in our study: the mudflat sites (sites E1–E12) and agricultural sites (sites A1–A12) (Figure 1). The main crop is rapeseed, which is the world’s second most important oilseed crop. Soil samples were collected in April 2017 to a depth of 0–5 cm. At each sampling location, 3 replicates of soil samples were collected. Each replicate was arranged into two randomized blocks and then mixed. All the sampled soils were sieved ( 0.99), indicating no significant effect of PCR inhibitors on gene quantification. Standards for qPCR were generated using a serial dilution of known copies of PCR fragments of the respective functional gene generated using M13 PCR from clones. Standard curves, spanning 107 -101 , were constructed by a dilution series of plasmids harboring the amoA gene. The plasmid was extracted by the Plasmid Purification Kit (Takara) and the concentration was measured by a NanoDrop ND-1000 UV-Vis Spectrophotometer and used for the calculation of standard copy numbers. The amplification efficiency ranged


Pyrosequencing Universal primer pair Tag-515F and 907R (Turner et al., 1999) were used to amplify soil bacterial 16S rRNA gene fragments for the MiSeq Illumina Sequencing Platform. PCR was carried out in 50-µl reaction mixtures containing each deoxynucleoside triphosphate at a concentration of 1.25 mM, 1 µl of forward and reverse primers (20 mM), 2U of Taq DNA polymerase (TaKaRa, Japan), and 50 ng of DNA. The following cycling parameters were used: 5 min of incubation at 94◦ C, followed by 32 cycles of 94◦ C for 30 s, 55◦ C for 30 s, and 72◦ C for 45 s, and a 10 min extension at 72◦ C (Supplementary Table S2). Triplicate reaction mixtures per sample were pooled together and purified using an agarose gel DNA purification kit (TaKaRa), and quantified using NanoDrop ND-1000 (Thermo Scientific, United States). The bar-coded PCR products were pooled in equimolar amounts (10 pg for each sample) before sequencing as described in Xiang et al. (2016). Sequences were merged by FLASH (Mago and Salzberg, 2011) and then processed using sequence data through the program AmpliconNoise, version 1.24, for the detection and correction of probable errors (Quince et al., 2011), obtainable from Quantitative Insights Into Microbial Ecology (QIIME1 ) (Caporaso et al., 2010). Poor-quality sequences (below an 1

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average quality score of 25) and short sequences ( 0.05). The salinity was positively correlated with the concentration of NH4 + (P < 0.05). The organic matter content ranged from 8.08 to 16.8% along the estuarine sites (mean 11.5%), whereas the mean organic matter content for the agricultural sites was 21.0%. There was no significant difference in soil pH between the mudflat (pH 8.3–9.3) and agricultural (pH 7.9–9.4) sites.

organic matter and the potential nitrification rates were observed among the agricultural soils (P < 0.05), indicating that organic matter was the key factor influencing the potential nitrification rate in agricultural sites. Contrarily, no correlation was observed between environmental factors and the rates of nitrification at the mudflat sites.

Abundance of Ammonia Oxidizers The distribution pattern for the ammonia oxidizers was significantly different between the mudflat and agricultural soils (Figure 3B). Across all mudflat sites, the ammonia oxidizers’ communities were dominated by AOB (inferred from the amoA genes from AOB, ranging from 1.3 × 104 to 1.2 × 105 copies g−1 d.w.s), which were significantly more abundant than AOA (1.3 × 103 –3.4 × 103 copies g−1 d.w.s). At the majority of the agricultural sites (A1, A2, A3, A4, A5, A6, A7, A9, and A10), the abundance of archaeal amoA genes (6.1 × 103 –3.6 × 105 copies g−1 d.w.s) was significantly higher than the abundance of bacterial amoA genes (2.1 × 103 –2.1 × 105 copies g−1 d.w.s) (P < 0.05), whereas the abundance of bacterial amoA genes

Potential Rates of Nitrification The rate of nitrification at the agricultural sites ranged from 2.0 to 65.1 µg g−1 day−1 and was generally higher than the rates at the mudflat sites (0–10.3 µg g−1 day−1 ) (Figure 3A). The soil nitrification rates at the upper estuary sites (E7–E12) were significantly higher than those in the lower estuary sites (E1–E6). Strong positive correlations between the amount of soil


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was higher than the abundance of archaeal amoA genes at the other agricultural sites. The AOA:AOB ratios were between 0.01 and 0.17 at the mudflat sites and between 0.36 and 6.17 at the agricultural sites. There was no correlation between the abundance of archaea organisms and the potential nitrification rates.

abundances ranging from 42.8 to 68.4% and 10.5 to 39.6%, respectively. Changes in the distribution of phylotypes were also detected in the AOB communities. All the sequences of the AOB matched those of the well-described AOB in the Nitrosospira (OTUs 1, 2, 3, 4, 5, and 6) and Nitrosomonas (OTUs 7 and 8) lineages. A significant portion of the OTUs (OTU 1 at sites E1, E2, E3, E4, E5, E6, E11, and E12; OTU 6 at sites E7, E8, E9, and E10) detected at the mudflat sites belonged to the AOB Nitrosospira (ranging from 41.9 to 88.4% and 42.7 to 72.9%, respectively), whereas the AOB Nitrosomonas OTU 8 was dominant at the agricultural sites (ranging from 42.9 to 96.7%), except at site A1 (OTU 3) and A12 (OTU 2), where Nitrosospira was the major lineage. Non-metric multidimensional scaling (NMDS) analysis was used to demonstrate the structural divergence of the community composition and to show the community differentiation of AOA and AOB between the mudflat sites and the agricultural sites (Figure 6).

Community Structure of Ammonia Oxidizers The composition of the phylotypes of the ammonia oxidizers was determined by pyrosequencing samples taken from each of the sites. The 16S rRNA sequences of the ammonia oxidizers showed the presence of AOA (14 OTUs) (Figure 4) and AOB (8 OTUs) (Figure 5). The AOA OTUs could be classified into six clusters: four (OTUs 1, 2, 3, and 4) were related to the Group 1.1a cluster; one (OTU 5) was related to the Group 1.1a-associated cluster; and nine OTUs were related to the Group 1.1b cluster, including two (OTUs 6 and 7) related to the 54D9 cluster, four (OTUs 7, 8, 9, 10, and 11) related to the 29i4 cluster, one (OTU 12) falling within the 29i4related cluster and two (OTUs 13 and 14) that most likely matched the Nitrososphaera viennensis cluster. The majority of AOA communities in the mudflat sites were in Group 1.1a (including OTUs 1 and 2), a cluster well-known in marine environments, with relative abundances ranging from 67.7 to 98.4%. In contrast, the dominant AOA phylotype in agricultural soils fell within clusters 54D9 (OTU 6) and 29i4 (OTU 8), with

Contribution of Deterministic and Stochastic Processes Control Ammonia Oxidizers’ Community Composition To test whether dispersal limited or niche-based mechanisms better explained the assembly of ammonia oxidizers’ community composition in mudflat and agricultural sites, we calculated the

FIGURE 4 | Heat map showing the relatedness of the ammonia-oxidizing archaea (AOA) community structures in the analysis of the (A) mudflat and (B) agricultural sites based on the relative abundance of distinct lineages of ammonia-oxidizing archaea 16S rRNA genes analyzed using pyrosequencing. The relative abundance of each lineage in each soil is displayed as a heat map representation. The phylogenetic position of each representative operational taxonomic unit is shown in the phylogenetic tree on the left-hand side.


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FIGURE 5 | Heat map showing the relatedness of ammonia-oxidizing bacteria community structures in the analysis of the (A) mudflat and (B) agricultural sites based on the relative abundance of distinct lineages of ammonia-oxidizing bacteria 16S rRNA genes analyzed using pyrosequencing. The relative abundance of each lineage in each soil is displayed as a heat map representation. The phylogenetic position of each representative operational taxonomic unit is shown in the phylogenetic tree on the left-hand side.

NRI (Figure 7) and NTI (Supplementary Figure S1) for each single community. For the AOA and AOB, we found that the mean NRI and mean NTI were positive (Figure 7 and Supplementary Figure S1, P < 0.05), suggesting AOA and AOB communities in both mudflat and agricultural soils were more influenced by niche processes than dispersal limitation. For the AOA, the mean value of NRI in agricultural soils was higher than that in mudflat sites, whereas no significant difference of the mean NTI value was observed between mudflat and agricultural soils. In addition, the mean NRI value of AOA was above 2 in agricultural soils. For AOB, no differentiation of either the mean NRI or NTI value was observed between mudflat and agricultural soils, and the NRI and NTI scores in all samples were between −2 and 2. In order to establish which process controlled community dynamics at different spatial scales, βNTI values were determined. The results showed that a stochastic process was dominant at all the sites in our study (Supplementary Figure S2; value > −2 and

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